In texstudio pdf compilation works fine using pdflatex.But if I run cmd and pdflatex.exe with the same parameters, output pdf appears without hyperlinks (TOC and all hyperlinks in document are absent).

In cmd (c:\Program Files\MiKTeX 2.9\miktex\bin\x64>) I use the following command:

it would be better to add the file path to the Windows path variable, so Windows would find the original pdflatex.exe. I just don't know how to explain this for Windows, as I use Linux and Mac OS. But if it works for you, fine. Just to mention it for the case somebody else reads it.

Keep in mind that an update of TeX, which may update pdflatex.exe, may need to copy it again over the old one.

Well, you could make a batch file (.bat) which calls the original pdflatex.exe with arguments. Or does the whole translation of this document like written here.